Have you ever wondered how the analog components in PSoC are interconnected when you place them on the TopDesign and draw those lines using PSoC Creator. The fact is, PSoC Creator generates code to write to multitude of registers and does the connection for you. The code is generated by what is called CY_FITTER. This piece of code goes in to the boot code which is executed before your main.c execution begins.
Once all the register configuration is made, is there a way to visually look at the actual analog routing? Yes there is, watch this video here and learn how to do this, http://www.cypress.com/?rID=57718